A large number of point sources pose a threat to ground water resources. A new tool is presented which enables a uniform and transparent risk assessment and prioritisation of these point sources at the catchment scale. The tool integrates aquifer vulnerability mapping, site-specific mass flux estimates on a local scale from all the sources, and 3D catchment-scale fate and transport modelling. It handles point sources at various knowledge levels
and accounts for uncertainties. The tool estimates the impacts on the water supply in the catchment and provides an overall prioritisation of the sites using a flexible scoring system. The tool is successfully applied to two catchments in Denmark.